NDLI: Energetics of short hydrogen bonds in photoactive yellow protein

Content Provider	PubMed Central
Author	Saito, Keisuke Hiroshi, Ishikita
Abstract	Recent neutron diffraction studies of photoactive yellow protein (PYP) proposed that the H bond between protonated Glu46 and the chromophore [ionized p-coumaric acid (pCA)] was a low-barrier H bond (LBHB). Using the atomic coordinates of the high-resolution crystal structure, we analyzed the energetics of the short H bond by two independent methods: electrostatic pK a calculations and a quantum mechanical/molecular mechanical (QM/MM) approach. (i) In the QM/MM optimized geometry, we reproduced the two short H-bond distances of the crystal structure: Tyr42-pCA (2.50 Å) and Glu46-pCA (2.57 Å). However, the H atoms obviously belonged to the Tyr or Glu moieties, and were not near the midpoint of the donor and acceptor atoms. (ii) The potential-energy curves of the two H bonds resembled those of standard asymmetric double-well potentials, which differ from those of LBHB. (iii) The calculated pK a values for Glu46 and pCA were 8.6 and 5.4, respectively. The pK a difference was unlikely to satisfy the prerequisite for LBHB. (iv) The LBHB in PYP was originally proposed to stabilize the ionized pCA because deprotonated Arg52 cannot stabilize it. However, the calculated pK a of Arg52 and QM/MM optimized geometry suggested that Arg52 was protonated on the protein surface. The short H bond between Glu46 and ionized pCA in the PYP ground state could be simply explained by electrostatic stabilization without invoking LBHB.
Related Links	http://dx.doi.org/10.1073/pnas.1113599108
Ending Page	172
Page Count	6
Starting Page	167
File Format	PDF
ISSN	00278424
e-ISSN	10916490
Journal	Proceedings of the National Academy of Sciences of the United States of America
Issue Number	1
Volume Number	109
Language	English
Publisher	National Academy of Sciences
Publisher Date	2012-01-03
Access Restriction	Open
Rights Holder	National Academy of Sciences
Subject Keyword	General Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

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